Crystal structure of Schmallenberg orthobunyavirus nucleoprotein-RNA complex reveals a novel RNA sequestration mechanism [PDF]
, 2013 Schmallenberg virus (SBV) is a newly emerged orthobunyavirus (family Bunyaviridae) that has caused severe disease in the offspring of farm animals across Europe.
Richard M. Elliott +16 more
core +1 more source
Predicting Ion Binding Properties for RNA Tertiary Structures [PDF]
Biophysical Journal, 2010 Recent experiments pointed to the potential importance of ion correlation for multivalent ions such as Mg(2+) ions in RNA folding. In this study, we develop an all-atom model to predict the ion electrostatics in RNA folding. The model can treat ion correlation effects explicitly by considering an ensemble of discrete ion distributions.
Tan, Zhi-Jie, Chen, Shi-Jie
openaire +2 more sources
The k-junction motif in RNA structure [PDF]
, 2014 The k-junction is a structural motif in RNA comprising a three-way helical junction based upon kink turn (k-turn) architecture. A computer program written to examine relative helical orientation identified the three-way junction of the Arabidopsis TPP ...
Daldrop, Peter +7 more
core +1 more source
RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources
BMC Bioinformatics, 2021 Background RNA regulates a variety of biological functions by interacting with other molecules. The ligand often binds in the RNA pocket to trigger structural changes or functions.
Ting Zhou +3 more
doaj +1 more source
Automated motif extraction and classification in RNA tertiary structures [PDF]
RNA, 2008 We used a novel graph-based approach to extract RNA tertiary motifs. We cataloged them all and clustered them using an innovative graph similarity measure. We applied our method to three widely studied structures: Haloarcula marismortui 50S (H.m 50S), Escherichia coli 50S (E. coli 50S), and Thermus thermophilus 16S (T.th 16S) RNAs.
Djelloul, Mahassine, Denise, Alain
openaire +2 more sources
Discovery of small molecules that target a tertiary-structured RNA
Proceedings of the National Academy of Sciences, 2022 There is growing interest in therapeutic intervention that targets disease-relevant RNAs using small molecules. While there have been some successes in RNA-targeted small-molecule discovery, a deeper understanding of structure–activity relationships in pursuing these targets has remained elusive.
Elena Menichelli +16 more
openaire +2 more sources
Single-molecule chemical denaturation of riboswitches [PDF]
, 2013 To date, single-molecule RNA science has been developed almost exclusively around the effect of metal ions as folding promoters and stabilizers of the RNA structure.
St-Pierre, Patrick +16 more
core +1 more source
Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs. [PDF]
PLoS Computational Biology, 2017 Prediction of RNA tertiary structure from sequence is an important problem, but generating accurate structure models for even short sequences remains difficult.
Michael F Sloma, David H Mathews
doaj +1 more source
The Prediction of Tertiary Structure of RNA Based upon Secondary Structure by Using the Relaxation Method and Texture Mapping Method [PDF]
Journal of Systemics, Cybernetics and Informatics, 2013 In this paper, we propose a method to predict tertiary structure of an RNA sequence. Our prediction method would first find the secondary structure of the given RNA sequence.
C.C. Lin, R.C.T. Lee
doaj
Dissecting the influence of Mg2+ on 3D architecture and ligand-binding of the guanine-sensing riboswitch aptamer domain [PDF]
, 2010 Long-range tertiary interactions determine the three-dimensional structure of a number of metabolite-binding riboswitch RNA elements and were found to be important for their regulatory function. For the guanine-sensing riboswitch of the Bacillus subtilis
Wöhnert, Jens +3 more
core +1 more source